Search

Specimen‐based data have played a central role in documenting body‐size shifts as a possible response to global warming over the last century. Identification of the drivers and patterns of these trends requires comparisons across taxa, often through meta‐analyses; however, a lack of repeatability within and interoperability (i.e. the potential for a dataset to be augmented for future research) among published studies is a major obstacle.We reviewed published studies on mammal body‐size changes in the Anthropocene, focusing on those that used museum specimens to analyse body‐size trends over time in at least one species. We assessed these papers for repeatability and interoperability with the following criteria: raw data and specimen identifiers were published and accessible, measurements were unambiguously defined, and potential sex‐ and age‐based size differences among individuals were accounted for.Most published body‐size studies have low potential for replication or augmentation; only one of 27 met all of our criteria. Although these 27 papers collectively generated an estimated 51,790 new body‐size measurements, only 1.25% (649) could be repeated or readily used in further investigations, as the remainder did not include raw data and/or specimen identifiers.Based on these findings, we recommend the following best practices in the study of body‐size trends. First, authors should explicitly define and justify all measures of size and quantify measurement error and publish all data, including measurements and specimen catalogue numbers. In addition to complying with the fundamental scientific tenet of repeatability, this minimizes redundant handling and the concomitant risk of damage to irreplaceable and often fragile museum specimens. Second, authors should test and account for the effects of demography, as some dimensions can change throughout an individual's life. Adopting these practices will improve the quality of body‐size studies, enhance the utility of extended specimen data from natural history collections, and enable researchers to conduct more expansive investigations of size trends over time. [ABSTRACT FROM AUTHOR]

Aim: Madagascar is renowned for its exceptional species diversity and endemism. The island's mountainous regions are thought to have played a role in lineage and species diversification, but this has yet to be explored across taxonomic groups and a temporal context has not yet been identified. We tested whether montane regions have promoted population divergence in Madagascar's vertebrate fauna and, if so, whether these divergence events were contemporaneous. Location: Moist evergreen forests of Madagascar. Taxa: Small mammals and reptiles. Methods: We analysed mitochondrial DNA data from 20 small‐mammal and five reptile species widely distributed across Madagascar's moist evergreen forests. We used phylogenetic and population genetic analyses to identify major phylogeographic patterns, then used linear regression to determine if the strength of phylogeographic structure is related to taxon, body size or elevation. Finally, we tested whether or not divergence across highlands occurred synchronously in multiple species, and used simulations to assess the power of these analyses to accurately estimate divergence times. Results: We observed a shared phylogeographic pattern across multiple species that suggests Madagascar's northern, central and southern highlands have served as important regions of diversification on Madagascar. This pattern was recovered across taxa with varying body sizes and elevational distributions. We also identified four pulses of divergence between the northern and central highlands since the late Miocene, although simulations suggest that our empirical data cannot recover the number or timing of divergence events with high certainty. Finally, we observed several instances of deep intraspecific genetic splits, suggesting that several of the species we evaluated may represent cryptic species complexes. Main Conclusions: We identified a highland‐driven phylogeographic pattern plus several cases of cryptic endemism and recent speciation, which have important evolutionary and conservation implications. This work presents a new phylogeographic hypothesis for recent diversification on Madagascar, reaffirms the urgent need for continued collection of voucher specimens and illuminates areas of particular importance for safeguarding genetic diversity in one of the world's foremost and threatened biodiversity hotspots. [ABSTRACT FROM AUTHOR]

Madagascar's shrew tenrecs (Mammalia: Tenrecidae; Microgale, Nesogale) represent an excellent system for studying speciation. Most species are endemic to the island's eastern humid forests, a region renowned for high levels of biodiversity and a high rate of in situ diversification. We set out to understand the speciation dynamics in a clade of recently described taxa: Microgale fotsifotsy and M. soricoides, which have nearly identical distributions in the moist evergreen forest, and M. nasoloi, which occurs in the western dry deciduous forest. A phylogenetic analysis using mitochondrial DNA data recovered two distinct clades of M. fotsifotsy: a south clade that is sister to, and broadly sympatric with, M. soricoides, and a north clade that is sister to the dry‐forest and distantly allopatric species M. nasoloi. To better understand this result, we analysed cranioskeletal measurements and performed demographic analyses using nuclear sequence data from ultraconserved elements. Nuclear data did not support a sister relationship between M. soricoides and the south clade of M. fotsifotsy but did demonstrate introgression between these clades, which probably explains the discordance between nuclear and mitochondrial phylogenies. Demographic analyses also revealed the absence of gene flow between the north and south clades of M. fotsifotsy. Morphometric data revealed several major differences between M. soricoides and M. fotsifotsy, as well as more subtle differences between the two clades of M. fotsifotsy. In light of these results, we treat the south clade of M. fotsifotsy as a new candidate species. Our findings demonstrate the utility of integrating multiple data types to understand complex speciation histories, and contribute to a growing body of evidence that species diversity on Madagascar is underestimated. [ABSTRACT FROM AUTHOR]

Abstract: There are a number of ecogeographical “rules” that describe patterns of geographical variation among organisms. The island rule predicts that populations of larger mammals on islands evolve smaller mean body size than their mainland counterparts, whereas smaller‐bodied mammals evolve larger size. Bergmann's rule predicts that populations of a species in colder climates (generally at higher latitudes) have larger mean body sizes than conspecifics in warmer climates (at lower latitudes). These two rules are rarely tested together and neither has been rigorously tested in treeshrews, a clade of small‐bodied mammals in their own order (Scandentia) broadly distributed in mainland Southeast Asia and on islands throughout much of the Sunda Shelf. The common treeshrew, Tupaia glis, is an excellent candidate for study and was used to test these two rules simultaneously for the first time in treeshrews. This species is distributed on the Malay Peninsula and several offshore islands east, west, and south of the mainland. Using craniodental dimensions as a proxy for body size, we investigated how island size, distance from the mainland, and maximum sea depth between the mainland and the islands relate to body size of 13 insular T. glis populations while also controlling for latitude and correlation among variables. We found a strong negative effect of latitude on body size in the common treeshrew, indicating the inverse of Bergmann's rule. We did not detect any overall difference in body size between the island and mainland populations. However, there was an effect of island area and maximum sea depth on body size among island populations. Although there is a strong latitudinal effect on body size, neither Bergmann's rule nor the island rule applies to the common treeshrew. The results of our analyses demonstrate the necessity of assessing multiple variables simultaneously in studies of ecogeographical rules. [ABSTRACT FROM AUTHOR]

Aim Ecological niche models ( ENMs) are used widely in ecology, evolution, global change biology, but model uncertainty remains an underappreciated issue. Generally, either a single model from one algorithm or an ensemble of single models from different algorithms is used to provide a prediction. In addition to variability among algorithms, recent studies have shown the need to consider variability within a single algorithm, for example optimizing model complexity by tuning model settings. We present an ensemble ENM using a single-algorithm approach, while adjusting model settings to maximize performance. Location Madagascar. Methods We used maxent, bioclimatic variables and occurrence records of four species of Malagasy tenrecs (Family Tenrecidae). We calibrated and evaluated preliminary models using a jackknife approach, tuning two model settings to estimate optimal model complexity. We chose a suite of top-performing preliminary models and then generated a consensus prediction. Furthermore, we calculated the variability among predictions of the co-optimal models to indicate variation in geography (i.e. uncertainty). We then did the same after projecting the predictions to climatic estimates for the Last Glacial Maximum and the year 2070. Results The default settings were never identified as optimal for any of the four species. The model settings considered as the co-optimal solutions essentially led to the same evaluation statistics; however, they showed high variation in their geographic predictions for three of the four species. Additionally, variation among such models was greater when transferred across time. Main conclusions This approach likely can provide better predictions for a single algorithm as well as quantifications of within-algorithm uncertainty, qualities that are highly useful in interpreting reconstructed suitable areas or forecasts of potential range shifts under future climate change. Finally, this within-algorithm uncertainty can be integrated into a larger framework that considers variability due to other factors (e.g. related to input data, alternate algorithms or various Global circulation models). [ABSTRACT FROM AUTHOR]

Aim: Quantitatively evaluate the similarity of genomic variation and geography in five different alpine small mammals in Alaska, and use this quantitative assessment of concordance as a framework for refining hypotheses about the processes structuring population genetic variation in either a species-specific or shared manner. Location: Alaska and adjacent north-western Canada. Methods: For each taxon we generated 3500-7500 single-nucleotide polymorphisms and applied a Procrustes analysis to find an optimal transformation that maximizes the similarity between principal components analysis maps of genetic variation and geographical maps of sample locations. We generate stability maps using projected distributions from ecological niche models of the Last Glacial Maximum and the present. Results: Significant similarity between genes and geography exists across taxa. However, the extent to which geography is predictive of patterns of genetic variation not only differs among taxa, but the correspondence between genes and geography varies over space. Geographical areas where genetic structure aligns poorly with the geographical coordinates are of particular interest because they indicate regions where processes other than isolation by distance (IBD) have influenced genetic variation. The clustering of individuals according to their sample location does not support suppositions of admixture, despite the presumed high vagility of some species (e.g. arctic ground squirrels). Main conclusions: Genomic data indicate a more nuanced biogeographical history for the taxa than suggested by previous studies based on mtDNA alone. These include departures from IBD that are shared among taxa, which suggest some shared processes structuring genetic variation, including new potential ancestral source populations. In addition, some regions fit expectations of IBD where incremental migration and gene flow play a strong role in population structure, despite any ecological difference among taxa. Differences in dispersal capabilities do not result in different species-specific local patterns of population structure, at least at the sampling scale examined here. We highlight how the general fit to, as well as departures from, expectations for patterns of genetic variation based on the Procrustes analyses can be used to generate hypotheses about the underlying processes. [ABSTRACT FROM AUTHOR]

Identifying the genetic structure of a species and the factors that drive it is an important first step in modern population management, in part because populations evolving from separate ancestral sources may possess potentially different characteristics. This is especially true for climate-sensitive species such as pikas, where the delimitation of distinct genetic units and the characterization of population responses to contemporary and historical environmental pressures are of particular interest. We combined a restriction site-associated DNA sequencing ( RADSeq) data set containing 4156 single nucleotide polymorphisms with ecological niche models ( ENMs) of present and past habitat suitability to characterize population composition and evaluate the effects of historical range shifts, contemporary climates and landscape factors on gene flow in Collared Pikas, which are found in Alaska and adjacent regions of northwestern Canada and are the lesser-studied of North America's two pika species. The results suggest that contemporary environmental factors contribute little to current population connectivity. Instead, genetic diversity is strongly shaped by the presence of three ancestral lineages isolated during the Pleistocene (~148 and 52 kya). Based on ENMs and genetic data, populations originating from a northern refugium experienced longer-term stability, whereas both southern lineages underwent population expansion - contradicting the southern stability and northern expansion patterns seen in many other taxa. Current populations are comparable with respect to generally low diversity within populations and little-to-no recent admixture. The predominance of divergent histories structuring populations implies that if we are to understand and manage pika populations, we must specifically assess and accurately account for the forces underlying genetic similarity. [ABSTRACT FROM AUTHOR]

Aim Pikas ( Ochotona spp.) are alpine specialists that show considerable morphological and genetic variation structured along latitudinal and elevational gradients. Recent studies of North American and Asian pikas have uncovered phylogeographical partitioning among separate mountain ranges and drainages, driven by Quaternary climate fluctuations. We tested the prediction that collared pikas ( O. collaris) exhibit lower genetic diversity and less structure than other species of pika due to lower long-term habitat stability. Location Eastern Beringia ( Alaska and north-western Canada). Methods We examined phylogeographical variation in the collared pika ( O. collaris) throughout much of its known range using the mitochondrial cytochrome b gene. Population divergence and genetic diversity were compared within and between mountain ranges. Genetic diversity was contrasted with current and Pleistocene habitat fragmentation inferred from ecological niche models. Results Low but significant differentiation was evident between most populations of O. collaris, with little haplotype sharing among populations and a single phylogeographical break separating a genetically distinct haplogroup in the south-eastern part of its range. Variation was mostly structured within populations (as opposed to between populations or mountain ranges). When within-species nucleotide diversity in O. collaris, O. princeps and O. curzoniae was compared, genetic diversity was found to decline with increasing latitude. Main conclusions Populations of O. collaris are less geographically structured and exhibit less variability than populations of either O. princeps or O. curzoniae. This pattern is better explained by the amount of available Pleistocene habitat predicted for each species than by current predicted habitat or population discontinuity. Collared pikas are currently considered to be a common species at low risk of extinction, but their habitat specificity, population subdivision, and low genetic variation may have consequences for their continued viability in a warming world. [ABSTRACT FROM AUTHOR]

Aim Capuchin monkey species are widely distributed across Central and South America. Morphological studies consistently divide the clade into robust and gracile forms, which show extensive sympatry in the Amazon Basin. We use genetic data to test whether Miocene or Plio-Pleistocene processes may explain capuchin species' present distributions, and consider three possible scenarios to explain widespread sympatry. Location The Neotropics, including the Amazon and Atlantic Coastal Forest. Methods We sequenced the 12S ribosomal RNA and cytochrome b genes from capuchin monkey specimens. The majority were sampled from US museum collections and were wild-caught individuals of known provenance across their distribution. We applied a Bayesian discrete-states diffusion model, which reconstructed the most probable history of invasion across nine subregions. We used comparative methods to test for phylogeographic association and dispersal rate variation. Results Capuchins contained two well supported monophyletic clades, the morphologically distinct 'gracile' and 'robust' groups. The time-tree analysis estimated a late Miocene divergence between Cebus and Sapajus and a subsequent Plio-Pleistocene diversification within each of the two clades. Bayesian analysis of phylogeographic diffusion history indicated that the current wide-ranging sympatry of Cebus and Sapajus across much of the Amazon Basin was the result of a single explosive late Pleistocene invasion of Sapajus from the Atlantic Forest into the Amazon, where Sapajus is now sympatric with gracile capuchins across much of their range. Main conclusions The biogeographic history of capuchins suggests late Miocene geographic isolation of the gracile and robust forms. Each form diversified independently, but during the Pleistocene, the robust Sapajus expanded its range from the Atlantic Forest to the Amazon, where it has now encroached substantially upon what was previously the exclusive range of gracile Cebus. The genus Cebus, as currently recognized, should be split into two genera to reflect the Miocene divergence and two subsequent independent Pliocene radiations: Cebus from the Amazon and Sapajus from the Atlantic Forest. [ABSTRACT FROM AUTHOR]

Aim  Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high-latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high-latitude arvicoline rodents. Location  Continental Alaska (alpine and arctic tundra) and the St Matthew Archipelago (Bering Sea). Methods  We generated and analysed cytochrome b sequences of 97 singing and insular voles ( M. miurus and M. abbreviatus) from Alaska. Deep evolutionary structure was inferred by phylogenetic analysis using parsimony, maximum likelihood and Bayesian approaches; the geographical structure of genetic diversity was assessed using analysis of molecular variance and network analysis; ages of cladogenetic and coalescent events were estimated using a relaxed molecular clock model with Bayesian approximation. Results  Regional nucleotide diversity in singing voles is higher than in other high-latitude arvicoline species, but intra-population diversity is within the observed range of values for arvicolines. Microtus abbreviatus specimens are phylogenetically nested within M. miurus. Molecular divergence date estimates indicate that current genetic diversity was formed in the last glacial (Wisconsinan) and previous interglacial (Sangamonian) periods, with the exception of a Middle Pleistocene split found between samples collected in the Wrangell Mountains region and all other singing vole samples. Main conclusions  High levels of phylogenetic and spatial structure are observed among analysed populations. This pattern is consistent with that expected for a taxon with a long history in Beringia. The spatial genetic structure of continental singing voles differs in its northern and southern ranges, possibly reflecting differences in habitat distribution between arctic and alpine tundra. Our phylogenetic results support the taxonomic inclusion of M. miurus in its senior synonym, M. abbreviatus. [ABSTRACT FROM AUTHOR]